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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttccattcatcatccatgcaggatagccatagcatatccatctaaatagaacctgaaccttgtgaaccaaattcttattgcag

Basic information

species Zea mays
transcript GRMZM2G153393_T01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g08550.2 (Oryza sativa), 5'ss of exon 14
CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttccattcatcatccatgcaggatagccatagcatatccatc------taaatagaac-------ctgaaccttgtgaaccaaattcttattgcag
|||||| ||||||||||| |||||||||||||| || |||||||| ||||| ||||| ||||| ||||| ||||| || || || ||  ||||||||||||||| | |||    ||||  | ||||||   ||| ||   |||   ||       || || ||||       ||||| ||| |||| ||||||| | || |||
CATCGATGCATTGGACAGAATGGTCGATCCTGCGCTGAAGGGTCTGTACCCTGCCAAGTCTCTCTCCCGGTTTGCCGACGTGCTCGCTTTGTGTGTCCAGgtaggatttca--ccatc--ctatgcagatgagctatgcaatactaattacctaatacatggaacagaatgtctgaatcttatgaaacaaattcatgttacag

upper sequence: GRMZM2G153393_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 15
CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttccattcatcatcca---tgcaggatagccatagcatatccatctaaatagaacctgaaccttgtgaaccaaattcttattgcag--------------------
|||||| ||  |||  |  ||||| ||||| |||||||| || || ||||||| ||| ||||| ||| | || ||||||||  |||| |||||||||||||||     |  | | |   |  |   ||||| || |    | |||  |  | | |   |   ||||   |   || |     ||| |||  |                     
CATCGATGCTCTGGCTAAAATGGTTGATCCGGCACTCAAAGGGCTCTACCCAGTCAAGTCTCTCTCCAGGTTCGCTGATGTGATTGCTCTGTGTGTCCAGgtaaggtgtttagttaaagtaaagagtgcag-atggattcatcat-cctgtttcagctg---ctgatggtaaagatctgttctctgattttaatattttatcgttttgggcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211336842|gb|FL296073.1|FL296073
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|40303178|gb|CK347565.1|CK347565
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|149106214|gb|EE291907.2|EE291907
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|40303248|gb|CK347635.1|CK347635
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|18177140|gb|BM378350.1|BM378350
EST:     CAGCCAAATCTCTATCCCGATTTGATGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|32845826|gb|CD985507.1|CD985507
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|211334695|gb|FL296071.1|FL296071
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAG
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAG
EST: gi|67014194|gb|CO442943.1|CO442943
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|28390198|gb|CB250095.1|CB250095
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCCCCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|211334696|gb|FL296072.1|FL296072
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|71442374|gb|DR823424.1|DR823424
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|60395662|gb|DN228532.1|DN228532
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|32838090|gb|CD977768.1|CD977768
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|32847053|gb|CD986734.1|CD986734
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGCCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|213182930|gb|FM185306.1|FM185306
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|211334693|gb|FL296069.1|FL296069
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|32848553|gb|CD988234.1|CD988234
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|101390185|gb|EB817025.1|EB817025
EST:     CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGGGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|32847233|gb|CD986914.1|CD986914
EST:     CAGCTAAATCTCTATCCCGATTTGCTGATGCCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: CAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
EST: gi|6095509|gb|AW120176.1|AW120176
EST:     GATTTGCTGATGTCCTTGCCCTGTGTGTCCAG                         CCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT
genomic: GATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 122

CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTTCGACTTGTGCAGAGGGCCAACATGACGAAGAGGATGCTTGATGGGGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTTCGACTTGTGCAGAGGGCCAACATGACGAAGAGGATGCTTGATGGGGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTTCGACTTGTGCAGAGGGCCAACATGACGAAGAGGATGCTTGATGGGGATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttc ... cttattgcagCCTGAACCAGAATTCAGGCCACCAATGTCAGAGGTGGTGCAAGCATTGGTTCGACTTGTGCAGAGGGCCAACATGACGAAGAGGATGCTTGATGGGGATA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCGACGCATTGGACAGGATGGTCGATCCTGCACTCAAGGGTCTATACCCAGCCAAATCTCTATCCCGATTTGCTGATGTCCTTGCCCTGTGTGTCCAGgtagcagttccattcatcatccatgcaggatagccatagcatatccatctaaatagaacctgaaccttgtgaaccaaattcttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT